-
Notifications
You must be signed in to change notification settings - Fork 3
/
example3_fit.bngl
106 lines (70 loc) · 2.63 KB
/
example3_fit.bngl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
# K1__FREE__ changed to 0.313300979502126
# K2__FREE__ changed to 5.34931086e+01
# alpha__FREE__ changed to 8.32577586e-01
# End of permute change log
begin model
# Reference:
# 1. Monine MI et al. (2010) Biophys J 98: 48-56. <-- model and fitting results
# 2. Posner RG et al. (2007) Org Lett 9: 3551-3554. <-- data
begin parameters
K1__FREE__ 0.313300979502126 # Free parameter inserted by GenFit
K2__FREE__ 5.34931086e+01 # Free parameter inserted by GenFit
alpha__FREE__ 8.32577586e-01 # Free parameter inserted by GenFit
# Avogadro constant
NA 6.02214e23 # [=] molecules per mol
# fraction of a cell to consider in a stochastic simulation
f 0.001 # [=] dimensionless, from Table 1 in Ref 1
chi=1.0/f
# cell density
cellDensity 1.0e9 # [=] cells per L (1e6 cells per ml), from Table 1 in Ref 1
# volume of ECF surrounding a single cell (on average)
Vref=f/cellDensity # [=] L, from Table 1 in Ref 1
LTconc 7.0 # [=] nM
RTref f*3.0e5 # [=] molecules per cell, from Table 1 in Ref 1
LTref = LTconc*1.0e-9*(NA*Vref) # [=] ~4,200,000 molecules per cell, cf. Table 1 in Ref 1
RTconc = RTref*1.0e9/(NA*Vref) # [=] nM
# dissociation rate constants (settings are arbitrary)
koff 0.01 # [=] /s, from Table 1 in Ref
kr1=koff # [=] /s
kr2=koff # [=] /s
alpha alpha__FREE__
inverse_alpha=1.0/alpha # 1/alpha
K1 K1__FREE__ # [=] /nM, from Brandon
K2 K2__FREE__ # [=] /nM, from Brandon
kf1=K1*1.0e9*kr1/(NA*Vref) # [=] /(molecule/cell)/s
kf2=K2*1.0e9*kr2/(NA*Vref) # [=] /(molecule/cell)/s
end parameters
begin molecule types
L(s,s,s)
R(s,s)
end molecule types
begin seed species
L(s,s,s) LTref
R(s,s) RTref
end seed species
begin observables
Molecules R_total R()
Molecules L_total L()
Species L_free L(s,s,s)
end observables
begin functions
lambda() (L_total-L_free)/(2.0*R_total) # [=] dimensionless, (0,1)
FL() inverse_alpha*(L_total-L_free)/(2.0*R_total) # FL = lambda/alpha or lambda = alpha*FL
# I am multiplying by the inverse of alpha instead of dividing by alpha
# to avoid a "divide by zero" error
end functions
begin reaction rules
L(s,s,s)+R(s)->L(s!1,s,s).R(s!1) kf1
L(s!+,s)+R(s)->L(s!+,s!1).R(s!1) kf2
L(s!1).R(s!1)->L(s)+R(s) koff
end reaction rules
end model
begin actions
parameter_scan({parameter=>"LTconc",\
par_scan_vals=>[0.0005006902,0.001362623,0.0044341334,0.0149210839,\
0.0441574,0.1507897315,0.5013619944,1.5652727704,5.2257161826,\
16.9016532291,67.9604112309,213.4593409505],\
method=>"nf",complex=>1,gml=>10000000,print_functions=>1,\
t_start=>0,t_end=>5000,n_steps=>10,suffix=>"example3",\
steady_state=>1,get_final_state=>0})
end actions